OpenRaiser/Intern-Atlas huggingface dataset:
nD-PDPA: nDimensional Probability Density Profile Analysis
Venue: arXiv cs.CV 2023
Year: 2023

Despite the recent advances in various Structural Genomics Projects, a large gap remains between the number of sequenced and structurally characterized proteins. Some reasons for this discrepancy include technical difficulties, labor, and the cost related to determining a structure by experimental methods such as NMR spectroscopy. Several computational methods have been developed to expand the applicability of NMR spectroscopy by addressing temporal and economical problems more efficiently. While these methods demonstrate successful outcomes to solve more challenging and structurally novel proteins, the cost has not been reduced significantly. Probability Density Profile Analysis (PDPA) has been previously introduced by our lab to directly address the economics of structure determination of routine proteins and the identification of novel structures from a minimal set of unassigned NMR data. 2D-PDPA (in which 2D denotes incorporation of data from two alignment media) has been successful in identifying the structural homolog of an unknown protein within a library of ~1000 decoy structures. In order to further expand the selectivity and sensitivity of PDPA, the incorporation of additional data was necessary. However, the expansion of the original PDPA approach was limited by its computational requirements where the inclusion of additional data would render it computationally intractable. Here we present the most recent developments of PDPA method (nD-PDPA: n Dimensional Probability Density Profile Analysis) that eliminate 2D-PDPA's computational limitations, and allows inclusion of RDC data from multiple vector types in multiple alignment media.
To Asymmetry and Beyond: Structured Pruning of Sequence to Sequence Models for Improved Inference Efficiency
Venue: arXiv cs.CL 2023
Year: 2023

Sequence-to-sequence language models can be used to produce abstractive summaries which are coherent, relevant, and concise. Still, model sizes can make deployment in latency-sensitive or web-scale implementations difficult. This paper studies the relationship between model size, structured pruning, inference efficiency, and summarization accuracy on widely used summarization datasets. We show that model accuracy is tied to the encoder size while inference efficiency is connected to the decoder. Using asymmetric pruning can lead to nearly 3x improvement in inference latency with ~1 point loss in Rouge-2. Moreover, we find both the average degradation and the role of asymmetry to be consistent across model sizes and variations in datasets.
Learning Stability Attention in Vision-based End-to-end Driving Policies
Venue: arXiv cs.RO 2023
Year: 2023

Modern end-to-end learning systems can learn to explicitly infer control from perception. However, it is difficult to guarantee stability and robustness for these systems since they are often exposed to unstructured, high-dimensional, and complex observation spaces (e.g., autonomous driving from a stream of pixel inputs). We propose to leverage control Lyapunov functions (CLFs) to equip end-to-end vision-based policies with stability properties and introduce stability attention in CLFs (att-CLFs) to tackle environmental changes and improve learning flexibility. We also present an uncertainty propagation technique that is tightly integrated into att-CLFs. We demonstrate the effectiveness of att-CLFs via comparison with classical CLFs, model predictive control, and vanilla end-to-end learning in a photo-realistic simulator and on a real full-scale autonomous vehicle.
Core Challenges in Embodied Vision-Language Planning
Venue: arXiv cs.RO 2023
Year: 2023

Recent advances in the areas of Multimodal Machine Learning and Artificial Intelligence (AI) have led to the development of challenging tasks at the intersection of Computer Vision, Natural Language Processing, and Robotics. Whereas many approaches and previous survey pursuits have characterised one or two of these dimensions, there has not been a holistic analysis at the center of all three. Moreover, even when combinations of these topics are considered, more focus is placed on describing, e.g., current architectural methods, as opposed to also illustrating high-level challenges and opportunities for the field. In this survey paper, we discuss Embodied Vision-Language Planning (EVLP) tasks, a family of prominent embodied navigation and manipulation problems that jointly leverage computer vision and natural language for interaction in physical environments. We propose a taxonomy to unify these tasks and provide an in-depth analysis and comparison of the current and new algorithmic approaches, metrics, simulators, and datasets used for EVLP tasks. Finally, we present the core challenges that we believe new EVLP works should seek to address, and we advocate for task construction that enables model generalisability and furthers real-world deployment.
Adaptive Headway Motion Control and Motion Prediction for Safe Unicycle Motion Design
Venue: arXiv cs.RO 2023
Year: 2023

Differential drive robots that can be modeled as a kinematic unicycle are a standard mobile base platform for many service and logistics robots. Safe and smooth autonomous motion around obstacles is a crucial skill for unicycle robots to perform diverse tasks in complex environments. A classical control approach for unicycle control is feedback linearization using a headway point at a fixed headway distance in front of the unicycle. The unicycle headway control brings the headway point to a desired goal location by embedding a linear headway reference dynamics, which often results in an undesired offset for the actual unicycle position. In this paper, we introduce a new unicycle headway control approach with an adaptive headway distance that overcomes this limitation, i.e., when the headway point reaches the goal the unicycle position is also at the goal. By systematically analyzing the closed-loop unicycle motion under the adaptive headway controller, we design analytical feedback motion prediction methods that bound the closed-loop unicycle position trajectory and so can be effectively used for safety assessment and safe unicycle motion design around obstacles. We present an application of adaptive headway motion control and motion prediction for safe unicycle path following around obstacles in numerical simulations.
Inapproximability of sufficient reasons for decision trees
Venue: arXiv cs.CC 2023
Year: 2023

In this note, we establish the hardness of approximation of the problem of computing the minimal size of a $δ$-sufficient reason for decision trees.
Approach Intelligent Writing Assistants Usability with Seven Stages of Action
Venue: arXiv cs.HC 2023
Year: 2023

Despite the potential of Large Language Models (LLMs) as writing assistants, they are plagued by issues like coherence and fluency of the model output, trustworthiness, ownership of the generated content, and predictability of model performance, thereby limiting their usability. In this position paper, we propose to adopt Norman's seven stages of action as a framework to approach the interaction design of intelligent writing assistants. We illustrate the framework's applicability to writing tasks by providing an example of software tutorial authoring. The paper also discusses the framework as a tool to synthesize research on the interaction design of LLM-based tools and presents examples of tools that support the stages of action. Finally, we briefly outline the potential of a framework for human-LLM interaction research.
Whose Text Is It Anyway? Exploring BigCode, Intellectual Property, and Ethics
Venue: arXiv cs.CY 2023
Year: 2023

Intelligent or generative writing tools rely on large language models that recognize, summarize, translate, and predict content. This position paper probes the copyright interests of open data sets used to train large language models (LLMs). Our paper asks, how do LLMs trained on open data sets circumvent the copyright interests of the used data? We start by defining software copyright and tracing its history. We rely on GitHub Copilot as a modern case study challenging software copyright. Our conclusion outlines obstacles that generative writing assistants create for copyright, and offers a practical road map for copyright analysis for developers, software law experts, and general users to consider in the context of intelligent LLM-powered writing tools.
Synthetic Sample Selection for Generalized Zero-Shot Learning
Venue: arXiv cs.CV 2023
Year: 2023

Generalized Zero-Shot Learning (GZSL) has emerged as a pivotal research domain in computer vision, owing to its capability to recognize objects that have not been seen during training. Despite the significant progress achieved by generative techniques in converting traditional GZSL to fully supervised learning, they tend to generate a large number of synthetic features that are often redundant, thereby increasing training time and decreasing accuracy. To address this issue, this paper proposes a novel approach for synthetic feature selection using reinforcement learning. In particular, we propose a transformer-based selector that is trained through proximal policy optimization (PPO) to select synthetic features based on the validation classification accuracy of the seen classes, which serves as a reward. The proposed method is model-agnostic and data-agnostic, making it applicable to both images and videos and versatile for diverse applications. Our experimental results demonstrate the superiority of our approach over existing feature-generating methods, yielding improved overall performance on multiple benchmarks.
Affect as a proxy for literary mood
Venue: arXiv cs.CL 2023
Year: 2023

We propose to use affect as a proxy for mood in literary texts. In this study, we explore the differences in computationally detecting tone versus detecting mood. Methodologically we utilize affective word embeddings to look at the affective distribution in different text segments. We also present a simple yet efficient and effective method of enhancing emotion lexicons to take both semantic shift and the domain of the text into account producing real-world congruent results closely matching both contemporary and modern qualitative analyses.
FengWu: Pushing the Skillful Global Medium-range Weather Forecast beyond 10 Days Lead
Venue: arXiv cs.AI 2023
Year: 2023

We present FengWu, an advanced data-driven global medium-range weather forecast system based on Artificial Intelligence (AI). Different from existing data-driven weather forecast methods, FengWu solves the medium-range forecast problem from a multi-modal and multi-task perspective. Specifically, a deep learning architecture equipped with model-specific encoder-decoders and cross-modal fusion Transformer is elaborately designed, which is learned under the supervision of an uncertainty loss to balance the optimization of different predictors in a region-adaptive manner. Besides this, a replay buffer mechanism is introduced to improve medium-range forecast performance. With 39-year data training based on the ERA5 reanalysis, FengWu is able to accurately reproduce the atmospheric dynamics and predict the future land and atmosphere states at 37 vertical levels on a 0.25° latitude-longitude resolution. Hindcasts of 6-hourly weather in 2018 based on ERA5 demonstrate that FengWu performs better than GraphCast in predicting 80\% of the 880 reported predictands, e.g., reducing the root mean square error (RMSE) of 10-day lead global z500 prediction from 733 to 651 $m^{2}/s^2$. In addition, the inference cost of each iteration is merely 600ms on NVIDIA Tesla A100 hardware. The results suggest that FengWu can significantly improve the forecast skill and extend the skillful global medium-range weather forecast out to 10.75 days lead (with ACC of z500 > 0.6) for the first time.
When approximate design for fast homomorphic computation provides differential privacy guarantees
Venue: arXiv cs.CR 2023
Year: 2023

While machine learning has become pervasive in as diversified fields as industry, healthcare, social networks, privacy concerns regarding the training data have gained a critical importance. In settings where several parties wish to collaboratively train a common model without jeopardizing their sensitive data, the need for a private training protocol is particularly stringent and implies to protect the data against both the model's end-users and the actors of the training phase. Differential privacy (DP) and cryptographic primitives are complementary popular countermeasures against privacy attacks. Among these cryptographic primitives, fully homomorphic encryption (FHE) offers ciphertext malleability at the cost of time-consuming operations in the homomorphic domain. In this paper, we design SHIELD, a probabilistic approximation algorithm for the argmax operator which is both fast when homomorphically executed and whose inaccuracy is used as a feature to ensure DP guarantees. Even if SHIELD could have other applications, we here focus on one setting and seamlessly integrate it in the SPEED collaborative training framework from "SPEED: Secure, PrivatE, and Efficient Deep learning" (Grivet Sébert et al., 2021) to improve its computational efficiency. After thoroughly describing the FHE implementation of our algorithm and its DP analysis, we present experimental results. To the best of our knowledge, it is the first work in which relaxing the accuracy of an homomorphic calculation is constructively usable as a degree of freedom to achieve better FHE performances.
On the Limits of Cross-Authentication Checks for GNSS Signals
Venue: arXiv cs.CR 2023
Year: 2023

Global navigation satellite systems (GNSSs) are implementing security mechanisms: examples are Galileo open service navigation message authentication (OS-NMA) and GPS chips-message robust authentication (CHIMERA). Each of these mechanisms operates in a single band. However, nowadays, even commercial GNSS receivers typically compute the position, velocity, and time (PVT) solution using multiple constellations and signals from multiple bands at once, significantly improving both accuracy and availability. Hence, cross-authentication checks have been proposed, based on the PVT obtained from the mixture of authenticated and non-authenticated signals. In this paper, first, we formalize the models for the cross-authentication checks. Next, we describe, for each check, a spoofing attack to generate a fake signal leading the victim to a target PVT without notice. We analytically relate the degrees of the freedom of the attacker in manipulating the victim's solution to both the employed security checks and the number of open signals that can be tampered with by the attacker. We test the performance of the considered attack strategies on an experimental dataset. Lastly, we show the limits of the PVT-based GNSS cross-authentication checks, where both authenticated and non-authenticated signals are used.
An experimental study in Real-time Facial Emotion Recognition on new 3RL dataset
Venue: arXiv cs.CV 2023
Year: 2023

Although real-time facial emotion recognition is a hot topic research domain in the field of human-computer interaction, state-of the-art available datasets still suffer from various problems, such as some unrelated photos such as document photos, unbalanced numbers of photos in each class, and misleading images that can negatively affect correct classification. The 3RL dataset was created, which contains approximately 24K images and will be publicly available, to overcome previously available dataset problems. The 3RL dataset is labelled with five basic emotions: happiness, fear, sadness, disgust, and anger. Moreover, we compared the 3RL dataset with other famous state-of-the-art datasets (FER dataset, CK+ dataset), and we applied the most commonly used algorithms in previous works, SVM and CNN. The results show a noticeable improvement in generalization on the 3RL dataset. Experiments have shown an accuracy of up to 91.4% on 3RL dataset using CNN where results on FER2013, CK+ are, respectively (approximately from 60% to 85%).
Formal Derivation of LU Factorization with Pivoting
Venue: arXiv cs.MS 2023
Year: 2023

The FLAME methodology for deriving linear algebra algorithms from specification, first introduced around 2000, has been successfully applied to a broad cross section of operations. An open question has been whether it can yield algorithms for the best-known operation in linear algebra, LU factorization with partial pivoting (Gaussian elimination with row swapping). This paper shows that it can.
Safe MDP Planning by Learning Temporal Patterns of Undesirable Trajectories and Averting Negative Side Effects
Venue: arXiv cs.LG 2023
Year: 2023

In safe MDP planning, a cost function based on the current state and action is often used to specify safety aspects. In the real world, often the state representation used may lack sufficient fidelity to specify such safety constraints. Operating based on an incomplete model can often produce unintended negative side effects (NSEs). To address these challenges, first, we associate safety signals with state-action trajectories (rather than just an immediate state-action). This makes our safety model highly general. We also assume categorical safety labels are given for different trajectories, rather than a numerical cost function, which is harder to specify by the problem designer. We then employ a supervised learning model to learn such non-Markovian safety patterns. Second, we develop a Lagrange multiplier method, which incorporates the safety model and the underlying MDP model in a single computation graph to facilitate agent learning of safe behaviors. Finally, our empirical results on a variety of discrete and continuous domains show that this approach can satisfy complex non-Markovian safety constraints while optimizing an agent's total returns, is highly scalable, and is also better than the previous best approach for Markovian NSEs.
Static Fuzzy Bag-of-Words: a lightweight sentence embedding algorithm
Venue: arXiv cs.CL 2023
Year: 2023

The introduction of embedding techniques has pushed forward significantly the Natural Language Processing field. Many of the proposed solutions have been presented for word-level encoding; anyhow, in the last years, new mechanism to treat information at an higher level of aggregation, like at sentence- and document-level, have emerged. With this work we address specifically the sentence embeddings problem, presenting the Static Fuzzy Bag-of-Word model. Our model is a refinement of the Fuzzy Bag-of-Words approach, providing sentence embeddings with a predefined dimension. SFBoW provides competitive performances in Semantic Textual Similarity benchmarks, while requiring low computational resources.
Is it conceivable that neurogenesis, neural Darwinism, and species evolution could all serve as inspiration for the creation of evolutionary deep neural networks?
Venue: arXiv cs.NE 2023
Year: 2023

Deep Neural Networks (DNNs) are built using artificial neural networks. They are part of machine learning methods that are capable of learning from data that have been used in a wide range of applications. DNNs are mainly handcrafted and they usually contain numerous layers. Research frontier has emerged that concerns automated construction of DNNs via evolutionary algorithms. This paper emphasizes the importance of what we call two-dimensional brain evolution and how it can inspire two dimensional DNN evolutionary modeling. We also highlight the connection between the dropout method which is widely-used in regularizing DNNs and neurogenesis of the brain, and how these concepts could benefit DNNs evolution.The paper concludes with several recommendations for enhancing the automatic construction of DNNs.
Improving Visual Question Answering Models through Robustness Analysis and In-Context Learning with a Chain of Basic Questions
Venue: arXiv cs.CV 2023
Year: 2023

Deep neural networks have been critical in the task of Visual Question Answering (VQA), with research traditionally focused on improving model accuracy. Recently, however, there has been a trend towards evaluating the robustness of these models against adversarial attacks. This involves assessing the accuracy of VQA models under increasing levels of noise in the input, which can target either the image or the proposed query question, dubbed the main question. However, there is currently a lack of proper analysis of this aspect of VQA. This work proposes a new method that utilizes semantically related questions, referred to as basic questions, acting as noise to evaluate the robustness of VQA models. It is hypothesized that as the similarity of a basic question to the main question decreases, the level of noise increases. To generate a reasonable noise level for a given main question, a pool of basic questions is ranked based on their similarity to the main question, and this ranking problem is cast as a LASSO optimization problem. Additionally, this work proposes a novel robustness measure, R_score, and two basic question datasets to standardize the analysis of VQA model robustness. The experimental results demonstrate that the proposed evaluation method effectively analyzes the robustness of VQA models. Moreover, the experiments show that in-context learning with a chain of basic questions can enhance model accuracy.
CoT-MAE v2: Contextual Masked Auto-Encoder with Multi-view Modeling for Passage Retrieval
Venue: arXiv cs.CL 2023
Year: 2023

Growing techniques have been emerging to improve the performance of passage retrieval. As an effective representation bottleneck pretraining technique, the contextual masked auto-encoder utilizes contextual embedding to assist in the reconstruction of passages. However, it only uses a single auto-encoding pre-task for dense representation pre-training. This study brings multi-view modeling to the contextual masked auto-encoder. Firstly, multi-view representation utilizes both dense and sparse vectors as multi-view representations, aiming to capture sentence semantics from different aspects. Moreover, multiview decoding paradigm utilizes both autoencoding and auto-regressive decoders in representation bottleneck pre-training, aiming to provide both reconstructive and generative signals for better contextual representation pretraining. We refer to this multi-view pretraining method as CoT-MAE v2. Through extensive experiments, we show that CoT-MAE v2 is effective and robust on large-scale passage retrieval benchmarks and out-of-domain zero-shot benchmarks.